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<h1 class="epydoc">Source Code for <a href="dadi.Demographics1D-module.html">Module dadi.Demographics1D</a></h1>
<pre class="py-src">
<a name="L1"></a><tt class="py-lineno">  1</tt>  <tt class="py-line"><tt class="py-docstring">"""</tt> </tt>
<a name="L2"></a><tt class="py-lineno">  2</tt>  <tt class="py-line"><tt class="py-docstring">Single population demographic models.</tt> </tt>
<a name="L3"></a><tt class="py-lineno">  3</tt>  <tt class="py-line"><tt class="py-docstring">"""</tt> </tt>
<a name="L4"></a><tt class="py-lineno">  4</tt>  <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">numpy</tt> </tt>
<a name="L5"></a><tt class="py-lineno">  5</tt>  <tt class="py-line"> </tt>
<a name="L6"></a><tt class="py-lineno">  6</tt>  <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-0" class="py-name" targets="Package dadi=dadi-module.html"><a title="dadi" class="py-name" href="#" onclick="return doclink('link-0', 'dadi', 'link-0');">dadi</a></tt> <tt class="py-keyword">import</tt> <tt id="link-1" class="py-name" targets="Module dadi.Numerics=dadi.Numerics-module.html"><a title="dadi.Numerics" class="py-name" href="#" onclick="return doclink('link-1', 'Numerics', 'link-1');">Numerics</a></tt><tt class="py-op">,</tt> <tt id="link-2" class="py-name" targets="Module dadi.PhiManip=dadi.PhiManip-module.html"><a title="dadi.PhiManip" class="py-name" href="#" onclick="return doclink('link-2', 'PhiManip', 'link-2');">PhiManip</a></tt><tt class="py-op">,</tt> <tt id="link-3" class="py-name" targets="Module dadi.Integration=dadi.Integration-module.html"><a title="dadi.Integration" class="py-name" href="#" onclick="return doclink('link-3', 'Integration', 'link-3');">Integration</a></tt> </tt>
<a name="L7"></a><tt class="py-lineno">  7</tt>  <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-4" class="py-name"><a title="dadi" class="py-name" href="#" onclick="return doclink('link-4', 'dadi', 'link-0');">dadi</a></tt><tt class="py-op">.</tt><tt id="link-5" class="py-name" targets="Module dadi.Spectrum_mod=dadi.Spectrum_mod-module.html"><a title="dadi.Spectrum_mod" class="py-name" href="#" onclick="return doclink('link-5', 'Spectrum_mod', 'link-5');">Spectrum_mod</a></tt> <tt class="py-keyword">import</tt> <tt id="link-6" class="py-name" targets="Variable dadi.Demographics1D.Spectrum=dadi.Spectrum_mod.Spectrum-class.html,Variable dadi.Demographics2D.Spectrum=dadi.Spectrum_mod.Spectrum-class.html,Class dadi.Spectrum_mod.Spectrum=dadi.Spectrum_mod.Spectrum-class.html"><a title="dadi.Demographics1D.Spectrum
dadi.Demographics2D.Spectrum
dadi.Spectrum_mod.Spectrum" class="py-name" href="#" onclick="return doclink('link-6', 'Spectrum', 'link-6');">Spectrum</a></tt> </tt>
<a name="L8"></a><tt class="py-lineno">  8</tt>  <tt class="py-line"> </tt>
<a name="snm"></a><div id="snm-def"><a name="L9"></a><tt class="py-lineno">  9</tt> <a class="py-toggle" href="#" id="snm-toggle" onclick="return toggle('snm');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="dadi.Demographics1D-module.html#snm">snm</a><tt class="py-op">(</tt><tt class="py-param">notused</tt><tt class="py-op">,</tt> <tt class="py-param">ns</tt><tt class="py-op">,</tt> <tt class="py-param">pts</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="snm-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="snm-expanded"><a name="L10"></a><tt class="py-lineno"> 10</tt>  <tt class="py-line">    <tt class="py-docstring">"""</tt> </tt>
<a name="L11"></a><tt class="py-lineno"> 11</tt>  <tt class="py-line"><tt class="py-docstring">    Standard neutral model.</tt> </tt>
<a name="L12"></a><tt class="py-lineno"> 12</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L13"></a><tt class="py-lineno"> 13</tt>  <tt class="py-line"><tt class="py-docstring">    ns = (n1,)</tt> </tt>
<a name="L14"></a><tt class="py-lineno"> 14</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L15"></a><tt class="py-lineno"> 15</tt>  <tt class="py-line"><tt class="py-docstring">    n1: Number of samples in resulting Spectrum</tt> </tt>
<a name="L16"></a><tt class="py-lineno"> 16</tt>  <tt class="py-line"><tt class="py-docstring">    pts: Number of grid points to use in integration.</tt> </tt>
<a name="L17"></a><tt class="py-lineno"> 17</tt>  <tt class="py-line"><tt class="py-docstring">    """</tt> </tt>
<a name="L18"></a><tt class="py-lineno"> 18</tt>  <tt class="py-line">    <tt class="py-name">xx</tt> <tt class="py-op">=</tt> <tt id="link-7" class="py-name"><a title="dadi.Numerics" class="py-name" href="#" onclick="return doclink('link-7', 'Numerics', 'link-1');">Numerics</a></tt><tt class="py-op">.</tt><tt class="py-name">default_grid</tt><tt class="py-op">(</tt><tt class="py-name">pts</tt><tt class="py-op">)</tt> </tt>
<a name="L19"></a><tt class="py-lineno"> 19</tt>  <tt class="py-line">    <tt class="py-name">phi</tt> <tt class="py-op">=</tt> <tt id="link-8" class="py-name"><a title="dadi.PhiManip" class="py-name" href="#" onclick="return doclink('link-8', 'PhiManip', 'link-2');">PhiManip</a></tt><tt class="py-op">.</tt><tt id="link-9" class="py-name" targets="Function dadi.PhiManip.phi_1D()=dadi.PhiManip-module.html#phi_1D"><a title="dadi.PhiManip.phi_1D" class="py-name" href="#" onclick="return doclink('link-9', 'phi_1D', 'link-9');">phi_1D</a></tt><tt class="py-op">(</tt><tt class="py-name">xx</tt><tt class="py-op">)</tt> </tt>
<a name="L20"></a><tt class="py-lineno"> 20</tt>  <tt class="py-line"> </tt>
<a name="L21"></a><tt class="py-lineno"> 21</tt>  <tt class="py-line">    <tt class="py-name">fs</tt> <tt class="py-op">=</tt> <tt id="link-10" class="py-name"><a title="dadi.Demographics1D.Spectrum
dadi.Demographics2D.Spectrum
dadi.Spectrum_mod.Spectrum" class="py-name" href="#" onclick="return doclink('link-10', 'Spectrum', 'link-6');">Spectrum</a></tt><tt class="py-op">.</tt><tt id="link-11" class="py-name" targets="Static Method dadi.Spectrum_mod.Spectrum.from_phi()=dadi.Spectrum_mod.Spectrum-class.html#from_phi"><a title="dadi.Spectrum_mod.Spectrum.from_phi" class="py-name" href="#" onclick="return doclink('link-11', 'from_phi', 'link-11');">from_phi</a></tt><tt class="py-op">(</tt><tt class="py-name">phi</tt><tt class="py-op">,</tt> <tt class="py-name">ns</tt><tt class="py-op">,</tt> <tt class="py-op">(</tt><tt class="py-name">xx</tt><tt class="py-op">,</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L22"></a><tt class="py-lineno"> 22</tt>  <tt class="py-line">    <tt class="py-keyword">return</tt> <tt class="py-name">fs</tt> </tt>
</div><a name="L23"></a><tt class="py-lineno"> 23</tt>  <tt class="py-line"> </tt>
<a name="two_epoch"></a><div id="two_epoch-def"><a name="L24"></a><tt class="py-lineno"> 24</tt> <a class="py-toggle" href="#" id="two_epoch-toggle" onclick="return toggle('two_epoch');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="dadi.Demographics1D-module.html#two_epoch">two_epoch</a><tt class="py-op">(</tt><tt class="py-param">params</tt><tt class="py-op">,</tt> <tt class="py-param">ns</tt><tt class="py-op">,</tt> <tt class="py-param">pts</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="two_epoch-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="two_epoch-expanded"><a name="L25"></a><tt class="py-lineno"> 25</tt>  <tt class="py-line">    <tt class="py-docstring">"""</tt> </tt>
<a name="L26"></a><tt class="py-lineno"> 26</tt>  <tt class="py-line"><tt class="py-docstring">    Instantaneous size change some time ago.</tt> </tt>
<a name="L27"></a><tt class="py-lineno"> 27</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L28"></a><tt class="py-lineno"> 28</tt>  <tt class="py-line"><tt class="py-docstring">    params = (nu,T)</tt> </tt>
<a name="L29"></a><tt class="py-lineno"> 29</tt>  <tt class="py-line"><tt class="py-docstring">    ns = (n1,)</tt> </tt>
<a name="L30"></a><tt class="py-lineno"> 30</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L31"></a><tt class="py-lineno"> 31</tt>  <tt class="py-line"><tt class="py-docstring">    nu: Ratio of contemporary to ancient population size</tt> </tt>
<a name="L32"></a><tt class="py-lineno"> 32</tt>  <tt class="py-line"><tt class="py-docstring">    T: Time in the past at which size change happened (in units of 2*Na </tt> </tt>
<a name="L33"></a><tt class="py-lineno"> 33</tt>  <tt class="py-line"><tt class="py-docstring">       generations) </tt> </tt>
<a name="L34"></a><tt class="py-lineno"> 34</tt>  <tt class="py-line"><tt class="py-docstring">    n1: Number of samples in resulting Spectrum</tt> </tt>
<a name="L35"></a><tt class="py-lineno"> 35</tt>  <tt class="py-line"><tt class="py-docstring">    pts: Number of grid points to use in integration.</tt> </tt>
<a name="L36"></a><tt class="py-lineno"> 36</tt>  <tt class="py-line"><tt class="py-docstring">    """</tt> </tt>
<a name="L37"></a><tt class="py-lineno"> 37</tt>  <tt class="py-line">    <tt class="py-name">nu</tt><tt class="py-op">,</tt><tt class="py-name">T</tt> <tt class="py-op">=</tt> <tt class="py-name">params</tt> </tt>
<a name="L38"></a><tt class="py-lineno"> 38</tt>  <tt class="py-line"> </tt>
<a name="L39"></a><tt class="py-lineno"> 39</tt>  <tt class="py-line">    <tt class="py-name">xx</tt> <tt class="py-op">=</tt> <tt id="link-12" class="py-name"><a title="dadi.Numerics" class="py-name" href="#" onclick="return doclink('link-12', 'Numerics', 'link-1');">Numerics</a></tt><tt class="py-op">.</tt><tt class="py-name">default_grid</tt><tt class="py-op">(</tt><tt class="py-name">pts</tt><tt class="py-op">)</tt> </tt>
<a name="L40"></a><tt class="py-lineno"> 40</tt>  <tt class="py-line">    <tt class="py-name">phi</tt> <tt class="py-op">=</tt> <tt id="link-13" class="py-name"><a title="dadi.PhiManip" class="py-name" href="#" onclick="return doclink('link-13', 'PhiManip', 'link-2');">PhiManip</a></tt><tt class="py-op">.</tt><tt id="link-14" class="py-name"><a title="dadi.PhiManip.phi_1D" class="py-name" href="#" onclick="return doclink('link-14', 'phi_1D', 'link-9');">phi_1D</a></tt><tt class="py-op">(</tt><tt class="py-name">xx</tt><tt class="py-op">)</tt> </tt>
<a name="L41"></a><tt class="py-lineno"> 41</tt>  <tt class="py-line">     </tt>
<a name="L42"></a><tt class="py-lineno"> 42</tt>  <tt class="py-line">    <tt class="py-name">phi</tt> <tt class="py-op">=</tt> <tt id="link-15" class="py-name"><a title="dadi.Integration" class="py-name" href="#" onclick="return doclink('link-15', 'Integration', 'link-3');">Integration</a></tt><tt class="py-op">.</tt><tt id="link-16" class="py-name" targets="Function dadi.Integration.one_pop()=dadi.Integration-module.html#one_pop"><a title="dadi.Integration.one_pop" class="py-name" href="#" onclick="return doclink('link-16', 'one_pop', 'link-16');">one_pop</a></tt><tt class="py-op">(</tt><tt class="py-name">phi</tt><tt class="py-op">,</tt> <tt class="py-name">xx</tt><tt class="py-op">,</tt> <tt class="py-name">T</tt><tt class="py-op">,</tt> <tt class="py-name">nu</tt><tt class="py-op">)</tt> </tt>
<a name="L43"></a><tt class="py-lineno"> 43</tt>  <tt class="py-line"> </tt>
<a name="L44"></a><tt class="py-lineno"> 44</tt>  <tt class="py-line">    <tt class="py-name">fs</tt> <tt class="py-op">=</tt> <tt id="link-17" class="py-name"><a title="dadi.Demographics1D.Spectrum
dadi.Demographics2D.Spectrum
dadi.Spectrum_mod.Spectrum" class="py-name" href="#" onclick="return doclink('link-17', 'Spectrum', 'link-6');">Spectrum</a></tt><tt class="py-op">.</tt><tt id="link-18" class="py-name"><a title="dadi.Spectrum_mod.Spectrum.from_phi" class="py-name" href="#" onclick="return doclink('link-18', 'from_phi', 'link-11');">from_phi</a></tt><tt class="py-op">(</tt><tt class="py-name">phi</tt><tt class="py-op">,</tt> <tt class="py-name">ns</tt><tt class="py-op">,</tt> <tt class="py-op">(</tt><tt class="py-name">xx</tt><tt class="py-op">,</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L45"></a><tt class="py-lineno"> 45</tt>  <tt class="py-line">    <tt class="py-keyword">return</tt> <tt class="py-name">fs</tt> </tt>
</div><a name="L46"></a><tt class="py-lineno"> 46</tt>  <tt class="py-line"> </tt>
<a name="growth"></a><div id="growth-def"><a name="L47"></a><tt class="py-lineno"> 47</tt> <a class="py-toggle" href="#" id="growth-toggle" onclick="return toggle('growth');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="dadi.Demographics1D-module.html#growth">growth</a><tt class="py-op">(</tt><tt class="py-param">params</tt><tt class="py-op">,</tt> <tt class="py-param">ns</tt><tt class="py-op">,</tt> <tt class="py-param">pts</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="growth-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="growth-expanded"><a name="L48"></a><tt class="py-lineno"> 48</tt>  <tt class="py-line">    <tt class="py-docstring">"""</tt> </tt>
<a name="L49"></a><tt class="py-lineno"> 49</tt>  <tt class="py-line"><tt class="py-docstring">    Exponential growth beginning some time ago.</tt> </tt>
<a name="L50"></a><tt class="py-lineno"> 50</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L51"></a><tt class="py-lineno"> 51</tt>  <tt class="py-line"><tt class="py-docstring">    params = (nu,T)</tt> </tt>
<a name="L52"></a><tt class="py-lineno"> 52</tt>  <tt class="py-line"><tt class="py-docstring">    ns = (n1,)</tt> </tt>
<a name="L53"></a><tt class="py-lineno"> 53</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L54"></a><tt class="py-lineno"> 54</tt>  <tt class="py-line"><tt class="py-docstring">    nu: Ratio of contemporary to ancient population size</tt> </tt>
<a name="L55"></a><tt class="py-lineno"> 55</tt>  <tt class="py-line"><tt class="py-docstring">    T: Time in the past at which growth began (in units of 2*Na </tt> </tt>
<a name="L56"></a><tt class="py-lineno"> 56</tt>  <tt class="py-line"><tt class="py-docstring">       generations) </tt> </tt>
<a name="L57"></a><tt class="py-lineno"> 57</tt>  <tt class="py-line"><tt class="py-docstring">    n1: Number of samples in resulting Spectrum</tt> </tt>
<a name="L58"></a><tt class="py-lineno"> 58</tt>  <tt class="py-line"><tt class="py-docstring">    pts: Number of grid points to use in integration.</tt> </tt>
<a name="L59"></a><tt class="py-lineno"> 59</tt>  <tt class="py-line"><tt class="py-docstring">    """</tt> </tt>
<a name="L60"></a><tt class="py-lineno"> 60</tt>  <tt class="py-line">    <tt class="py-name">nu</tt><tt class="py-op">,</tt><tt class="py-name">T</tt> <tt class="py-op">=</tt> <tt class="py-name">params</tt> </tt>
<a name="L61"></a><tt class="py-lineno"> 61</tt>  <tt class="py-line"> </tt>
<a name="L62"></a><tt class="py-lineno"> 62</tt>  <tt class="py-line">    <tt class="py-name">xx</tt> <tt class="py-op">=</tt> <tt id="link-19" class="py-name"><a title="dadi.Numerics" class="py-name" href="#" onclick="return doclink('link-19', 'Numerics', 'link-1');">Numerics</a></tt><tt class="py-op">.</tt><tt class="py-name">default_grid</tt><tt class="py-op">(</tt><tt class="py-name">pts</tt><tt class="py-op">)</tt> </tt>
<a name="L63"></a><tt class="py-lineno"> 63</tt>  <tt class="py-line">    <tt class="py-name">phi</tt> <tt class="py-op">=</tt> <tt id="link-20" class="py-name"><a title="dadi.PhiManip" class="py-name" href="#" onclick="return doclink('link-20', 'PhiManip', 'link-2');">PhiManip</a></tt><tt class="py-op">.</tt><tt id="link-21" class="py-name"><a title="dadi.PhiManip.phi_1D" class="py-name" href="#" onclick="return doclink('link-21', 'phi_1D', 'link-9');">phi_1D</a></tt><tt class="py-op">(</tt><tt class="py-name">xx</tt><tt class="py-op">)</tt> </tt>
<a name="L64"></a><tt class="py-lineno"> 64</tt>  <tt class="py-line"> </tt>
<a name="L65"></a><tt class="py-lineno"> 65</tt>  <tt class="py-line">    <tt class="py-name">nu_func</tt> <tt class="py-op">=</tt> <tt class="py-keyword">lambda</tt> <tt class="py-name">t</tt><tt class="py-op">:</tt> <tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">exp</tt><tt class="py-op">(</tt><tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">log</tt><tt class="py-op">(</tt><tt class="py-name">nu</tt><tt class="py-op">)</tt> <tt class="py-op">*</tt> <tt class="py-name">t</tt><tt class="py-op">/</tt><tt class="py-name">T</tt><tt class="py-op">)</tt> </tt>
<a name="L66"></a><tt class="py-lineno"> 66</tt>  <tt class="py-line">    <tt class="py-name">phi</tt> <tt class="py-op">=</tt> <tt id="link-22" class="py-name"><a title="dadi.Integration" class="py-name" href="#" onclick="return doclink('link-22', 'Integration', 'link-3');">Integration</a></tt><tt class="py-op">.</tt><tt id="link-23" class="py-name"><a title="dadi.Integration.one_pop" class="py-name" href="#" onclick="return doclink('link-23', 'one_pop', 'link-16');">one_pop</a></tt><tt class="py-op">(</tt><tt class="py-name">phi</tt><tt class="py-op">,</tt> <tt class="py-name">xx</tt><tt class="py-op">,</tt> <tt class="py-name">T</tt><tt class="py-op">,</tt> <tt class="py-name">nu_func</tt><tt class="py-op">)</tt> </tt>
<a name="L67"></a><tt class="py-lineno"> 67</tt>  <tt class="py-line"> </tt>
<a name="L68"></a><tt class="py-lineno"> 68</tt>  <tt class="py-line">    <tt class="py-name">fs</tt> <tt class="py-op">=</tt> <tt id="link-24" class="py-name"><a title="dadi.Demographics1D.Spectrum
dadi.Demographics2D.Spectrum
dadi.Spectrum_mod.Spectrum" class="py-name" href="#" onclick="return doclink('link-24', 'Spectrum', 'link-6');">Spectrum</a></tt><tt class="py-op">.</tt><tt id="link-25" class="py-name"><a title="dadi.Spectrum_mod.Spectrum.from_phi" class="py-name" href="#" onclick="return doclink('link-25', 'from_phi', 'link-11');">from_phi</a></tt><tt class="py-op">(</tt><tt class="py-name">phi</tt><tt class="py-op">,</tt> <tt class="py-name">ns</tt><tt class="py-op">,</tt> <tt class="py-op">(</tt><tt class="py-name">xx</tt><tt class="py-op">,</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L69"></a><tt class="py-lineno"> 69</tt>  <tt class="py-line">    <tt class="py-keyword">return</tt> <tt class="py-name">fs</tt> </tt>
</div><a name="L70"></a><tt class="py-lineno"> 70</tt>  <tt class="py-line"> </tt>
<a name="bottlegrowth"></a><div id="bottlegrowth-def"><a name="L71"></a><tt class="py-lineno"> 71</tt> <a class="py-toggle" href="#" id="bottlegrowth-toggle" onclick="return toggle('bottlegrowth');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="dadi.Demographics1D-module.html#bottlegrowth">bottlegrowth</a><tt class="py-op">(</tt><tt class="py-param">params</tt><tt class="py-op">,</tt> <tt class="py-param">ns</tt><tt class="py-op">,</tt> <tt class="py-param">pts</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="bottlegrowth-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="bottlegrowth-expanded"><a name="L72"></a><tt class="py-lineno"> 72</tt>  <tt class="py-line">    <tt class="py-docstring">"""</tt> </tt>
<a name="L73"></a><tt class="py-lineno"> 73</tt>  <tt class="py-line"><tt class="py-docstring">    Instantanous size change followed by exponential growth.</tt> </tt>
<a name="L74"></a><tt class="py-lineno"> 74</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L75"></a><tt class="py-lineno"> 75</tt>  <tt class="py-line"><tt class="py-docstring">    params = (nuB,nuF,T)</tt> </tt>
<a name="L76"></a><tt class="py-lineno"> 76</tt>  <tt class="py-line"><tt class="py-docstring">    ns = (n1,)</tt> </tt>
<a name="L77"></a><tt class="py-lineno"> 77</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L78"></a><tt class="py-lineno"> 78</tt>  <tt class="py-line"><tt class="py-docstring">    nuB: Ratio of population size after instantanous change to ancient</tt> </tt>
<a name="L79"></a><tt class="py-lineno"> 79</tt>  <tt class="py-line"><tt class="py-docstring">         population size</tt> </tt>
<a name="L80"></a><tt class="py-lineno"> 80</tt>  <tt class="py-line"><tt class="py-docstring">    nuF: Ratio of contemporary to ancient population size</tt> </tt>
<a name="L81"></a><tt class="py-lineno"> 81</tt>  <tt class="py-line"><tt class="py-docstring">    T: Time in the past at which instantaneous change happened and growth began</tt> </tt>
<a name="L82"></a><tt class="py-lineno"> 82</tt>  <tt class="py-line"><tt class="py-docstring">       (in units of 2*Na generations) </tt> </tt>
<a name="L83"></a><tt class="py-lineno"> 83</tt>  <tt class="py-line"><tt class="py-docstring">    n1: Number of samples in resulting Spectrum</tt> </tt>
<a name="L84"></a><tt class="py-lineno"> 84</tt>  <tt class="py-line"><tt class="py-docstring">    pts: Number of grid points to use in integration.</tt> </tt>
<a name="L85"></a><tt class="py-lineno"> 85</tt>  <tt class="py-line"><tt class="py-docstring">    """</tt> </tt>
<a name="L86"></a><tt class="py-lineno"> 86</tt>  <tt class="py-line">    <tt class="py-name">nuB</tt><tt class="py-op">,</tt><tt class="py-name">nuF</tt><tt class="py-op">,</tt><tt class="py-name">T</tt> <tt class="py-op">=</tt> <tt class="py-name">params</tt> </tt>
<a name="L87"></a><tt class="py-lineno"> 87</tt>  <tt class="py-line"> </tt>
<a name="L88"></a><tt class="py-lineno"> 88</tt>  <tt class="py-line">    <tt class="py-name">xx</tt> <tt class="py-op">=</tt> <tt id="link-26" class="py-name"><a title="dadi.Numerics" class="py-name" href="#" onclick="return doclink('link-26', 'Numerics', 'link-1');">Numerics</a></tt><tt class="py-op">.</tt><tt class="py-name">default_grid</tt><tt class="py-op">(</tt><tt class="py-name">pts</tt><tt class="py-op">)</tt> </tt>
<a name="L89"></a><tt class="py-lineno"> 89</tt>  <tt class="py-line">    <tt class="py-name">phi</tt> <tt class="py-op">=</tt> <tt id="link-27" class="py-name"><a title="dadi.PhiManip" class="py-name" href="#" onclick="return doclink('link-27', 'PhiManip', 'link-2');">PhiManip</a></tt><tt class="py-op">.</tt><tt id="link-28" class="py-name"><a title="dadi.PhiManip.phi_1D" class="py-name" href="#" onclick="return doclink('link-28', 'phi_1D', 'link-9');">phi_1D</a></tt><tt class="py-op">(</tt><tt class="py-name">xx</tt><tt class="py-op">)</tt> </tt>
<a name="L90"></a><tt class="py-lineno"> 90</tt>  <tt class="py-line"> </tt>
<a name="L91"></a><tt class="py-lineno"> 91</tt>  <tt class="py-line">    <tt class="py-name">nu_func</tt> <tt class="py-op">=</tt> <tt class="py-keyword">lambda</tt> <tt class="py-name">t</tt><tt class="py-op">:</tt> <tt class="py-name">nuB</tt><tt class="py-op">*</tt><tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">exp</tt><tt class="py-op">(</tt><tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">log</tt><tt class="py-op">(</tt><tt class="py-name">nuF</tt><tt class="py-op">/</tt><tt class="py-name">nuB</tt><tt class="py-op">)</tt> <tt class="py-op">*</tt> <tt class="py-name">t</tt><tt class="py-op">/</tt><tt class="py-name">T</tt><tt class="py-op">)</tt> </tt>
<a name="L92"></a><tt class="py-lineno"> 92</tt>  <tt class="py-line">    <tt class="py-name">phi</tt> <tt class="py-op">=</tt> <tt id="link-29" class="py-name"><a title="dadi.Integration" class="py-name" href="#" onclick="return doclink('link-29', 'Integration', 'link-3');">Integration</a></tt><tt class="py-op">.</tt><tt id="link-30" class="py-name"><a title="dadi.Integration.one_pop" class="py-name" href="#" onclick="return doclink('link-30', 'one_pop', 'link-16');">one_pop</a></tt><tt class="py-op">(</tt><tt class="py-name">phi</tt><tt class="py-op">,</tt> <tt class="py-name">xx</tt><tt class="py-op">,</tt> <tt class="py-name">T</tt><tt class="py-op">,</tt> <tt class="py-name">nu_func</tt><tt class="py-op">)</tt> </tt>
<a name="L93"></a><tt class="py-lineno"> 93</tt>  <tt class="py-line"> </tt>
<a name="L94"></a><tt class="py-lineno"> 94</tt>  <tt class="py-line">    <tt class="py-name">fs</tt> <tt class="py-op">=</tt> <tt id="link-31" class="py-name"><a title="dadi.Demographics1D.Spectrum
dadi.Demographics2D.Spectrum
dadi.Spectrum_mod.Spectrum" class="py-name" href="#" onclick="return doclink('link-31', 'Spectrum', 'link-6');">Spectrum</a></tt><tt class="py-op">.</tt><tt id="link-32" class="py-name"><a title="dadi.Spectrum_mod.Spectrum.from_phi" class="py-name" href="#" onclick="return doclink('link-32', 'from_phi', 'link-11');">from_phi</a></tt><tt class="py-op">(</tt><tt class="py-name">phi</tt><tt class="py-op">,</tt> <tt class="py-name">ns</tt><tt class="py-op">,</tt> <tt class="py-op">(</tt><tt class="py-name">xx</tt><tt class="py-op">,</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L95"></a><tt class="py-lineno"> 95</tt>  <tt class="py-line">    <tt class="py-keyword">return</tt> <tt class="py-name">fs</tt> </tt>
</div><a name="L96"></a><tt class="py-lineno"> 96</tt>  <tt class="py-line"> </tt>
<a name="three_epoch"></a><div id="three_epoch-def"><a name="L97"></a><tt class="py-lineno"> 97</tt> <a class="py-toggle" href="#" id="three_epoch-toggle" onclick="return toggle('three_epoch');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="dadi.Demographics1D-module.html#three_epoch">three_epoch</a><tt class="py-op">(</tt><tt class="py-param">params</tt><tt class="py-op">,</tt> <tt class="py-param">ns</tt><tt class="py-op">,</tt> <tt class="py-param">pts</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="three_epoch-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="three_epoch-expanded"><a name="L98"></a><tt class="py-lineno"> 98</tt>  <tt class="py-line">    <tt class="py-docstring">"""</tt> </tt>
<a name="L99"></a><tt class="py-lineno"> 99</tt>  <tt class="py-line"><tt class="py-docstring">    params = (nuB,nuF,TB,TF)</tt> </tt>
<a name="L100"></a><tt class="py-lineno">100</tt>  <tt class="py-line"><tt class="py-docstring">    ns = (n1,)</tt> </tt>
<a name="L101"></a><tt class="py-lineno">101</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L102"></a><tt class="py-lineno">102</tt>  <tt class="py-line"><tt class="py-docstring">    nuB: Ratio of bottleneck population size to ancient pop size</tt> </tt>
<a name="L103"></a><tt class="py-lineno">103</tt>  <tt class="py-line"><tt class="py-docstring">    nuF: Ratio of contemporary to ancient pop size</tt> </tt>
<a name="L104"></a><tt class="py-lineno">104</tt>  <tt class="py-line"><tt class="py-docstring">    TB: Length of bottleneck (in units of 2*Na generations) </tt> </tt>
<a name="L105"></a><tt class="py-lineno">105</tt>  <tt class="py-line"><tt class="py-docstring">    TF: Time since bottleneck recovery (in units of 2*Na generations) </tt> </tt>
<a name="L106"></a><tt class="py-lineno">106</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L107"></a><tt class="py-lineno">107</tt>  <tt class="py-line"><tt class="py-docstring">    n1: Number of samples in resulting Spectrum</tt> </tt>
<a name="L108"></a><tt class="py-lineno">108</tt>  <tt class="py-line"><tt class="py-docstring">    pts: Number of grid points to use in integration.</tt> </tt>
<a name="L109"></a><tt class="py-lineno">109</tt>  <tt class="py-line"><tt class="py-docstring">    """</tt> </tt>
<a name="L110"></a><tt class="py-lineno">110</tt>  <tt class="py-line">    <tt class="py-name">nuB</tt><tt class="py-op">,</tt><tt class="py-name">nuF</tt><tt class="py-op">,</tt><tt class="py-name">TB</tt><tt class="py-op">,</tt><tt class="py-name">TF</tt> <tt class="py-op">=</tt> <tt class="py-name">params</tt> </tt>
<a name="L111"></a><tt class="py-lineno">111</tt>  <tt class="py-line"> </tt>
<a name="L112"></a><tt class="py-lineno">112</tt>  <tt class="py-line">    <tt class="py-name">xx</tt> <tt class="py-op">=</tt> <tt id="link-33" class="py-name"><a title="dadi.Numerics" class="py-name" href="#" onclick="return doclink('link-33', 'Numerics', 'link-1');">Numerics</a></tt><tt class="py-op">.</tt><tt class="py-name">default_grid</tt><tt class="py-op">(</tt><tt class="py-name">pts</tt><tt class="py-op">)</tt> </tt>
<a name="L113"></a><tt class="py-lineno">113</tt>  <tt class="py-line">    <tt class="py-name">phi</tt> <tt class="py-op">=</tt> <tt id="link-34" class="py-name"><a title="dadi.PhiManip" class="py-name" href="#" onclick="return doclink('link-34', 'PhiManip', 'link-2');">PhiManip</a></tt><tt class="py-op">.</tt><tt id="link-35" class="py-name"><a title="dadi.PhiManip.phi_1D" class="py-name" href="#" onclick="return doclink('link-35', 'phi_1D', 'link-9');">phi_1D</a></tt><tt class="py-op">(</tt><tt class="py-name">xx</tt><tt class="py-op">)</tt> </tt>
<a name="L114"></a><tt class="py-lineno">114</tt>  <tt class="py-line"> </tt>
<a name="L115"></a><tt class="py-lineno">115</tt>  <tt class="py-line">    <tt class="py-name">phi</tt> <tt class="py-op">=</tt> <tt id="link-36" class="py-name"><a title="dadi.Integration" class="py-name" href="#" onclick="return doclink('link-36', 'Integration', 'link-3');">Integration</a></tt><tt class="py-op">.</tt><tt id="link-37" class="py-name"><a title="dadi.Integration.one_pop" class="py-name" href="#" onclick="return doclink('link-37', 'one_pop', 'link-16');">one_pop</a></tt><tt class="py-op">(</tt><tt class="py-name">phi</tt><tt class="py-op">,</tt> <tt class="py-name">xx</tt><tt class="py-op">,</tt> <tt class="py-name">TB</tt><tt class="py-op">,</tt> <tt class="py-name">nuB</tt><tt class="py-op">)</tt> </tt>
<a name="L116"></a><tt class="py-lineno">116</tt>  <tt class="py-line">    <tt class="py-name">phi</tt> <tt class="py-op">=</tt> <tt id="link-38" class="py-name"><a title="dadi.Integration" class="py-name" href="#" onclick="return doclink('link-38', 'Integration', 'link-3');">Integration</a></tt><tt class="py-op">.</tt><tt id="link-39" class="py-name"><a title="dadi.Integration.one_pop" class="py-name" href="#" onclick="return doclink('link-39', 'one_pop', 'link-16');">one_pop</a></tt><tt class="py-op">(</tt><tt class="py-name">phi</tt><tt class="py-op">,</tt> <tt class="py-name">xx</tt><tt class="py-op">,</tt> <tt class="py-name">TF</tt><tt class="py-op">,</tt> <tt class="py-name">nuF</tt><tt class="py-op">)</tt> </tt>
<a name="L117"></a><tt class="py-lineno">117</tt>  <tt class="py-line"> </tt>
<a name="L118"></a><tt class="py-lineno">118</tt>  <tt class="py-line">    <tt class="py-name">fs</tt> <tt class="py-op">=</tt> <tt id="link-40" class="py-name"><a title="dadi.Demographics1D.Spectrum
dadi.Demographics2D.Spectrum
dadi.Spectrum_mod.Spectrum" class="py-name" href="#" onclick="return doclink('link-40', 'Spectrum', 'link-6');">Spectrum</a></tt><tt class="py-op">.</tt><tt id="link-41" class="py-name"><a title="dadi.Spectrum_mod.Spectrum.from_phi" class="py-name" href="#" onclick="return doclink('link-41', 'from_phi', 'link-11');">from_phi</a></tt><tt class="py-op">(</tt><tt class="py-name">phi</tt><tt class="py-op">,</tt> <tt class="py-name">ns</tt><tt class="py-op">,</tt> <tt class="py-op">(</tt><tt class="py-name">xx</tt><tt class="py-op">,</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L119"></a><tt class="py-lineno">119</tt>  <tt class="py-line">    <tt class="py-keyword">return</tt> <tt class="py-name">fs</tt> </tt>
</div><a name="L120"></a><tt class="py-lineno">120</tt>  <tt class="py-line"> </tt><script type="text/javascript">
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